Calculate dsrs for local authorities

library(tidyverse)
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library(devtools)
## Loading required package: usethis
URL <- "https://github.com/julianflowers12/test-and-trace/blob/master/create_case_dsr.R?raw=TRUE"

source_url(URL)
## ℹ SHA-1 hash of file is d8b2d76c5aa803f523bbee1237871b0d069040af
test <- case_dsrs_las(area = "ltla")
## Loading required package: data.table
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## `summarise()` regrouping output by 'Code', 'Name', 'gender', 'ageband' (override with `.groups` argument)
tail(test$dsr)
## # A tibble: 6 x 10
## # Groups:   areaName, date [6]
##   areaName date       total_count total_pop value lowercl uppercl confidence
##   <chr>    <date>           <int>     <dbl> <dbl>   <dbl>   <dbl> <chr>     
## 1 York     2020-11-16         350    421236  81.5    73.0    90.8 95%       
## 2 York     2020-11-17         323    421236  76.2    67.9    85.2 95%       
## 3 York     2020-11-18         301    421236  70.9    62.9    79.5 95%       
## 4 York     2020-11-19         288    421236  68.7    60.8    77.3 95%       
## 5 York     2020-11-20         276    421236  65.7    58.0    74.1 95%       
## 6 York     2020-11-21         277    421236  66.5    58.7    75.0 95%       
## # … with 2 more variables: statistic <chr>, method <chr>

Tier 1

unique(test$dsr$areaName)
##   [1] "Adur"                               
##   [2] "Allerdale"                          
##   [3] "Amber Valley"                       
##   [4] "Arun"                               
##   [5] "Ashfield"                           
##   [6] "Ashford"                            
##   [7] "Aylesbury Vale"                     
##   [8] "Babergh"                            
##   [9] "Barking and Dagenham"               
##  [10] "Barnet"                             
##  [11] "Barnsley"                           
##  [12] "Barrow-in-Furness"                  
##  [13] "Basildon"                           
##  [14] "Basingstoke and Deane"              
##  [15] "Bassetlaw"                          
##  [16] "Bath and North East Somerset"       
##  [17] "Bedford"                            
##  [18] "Bexley"                             
##  [19] "Birmingham"                         
##  [20] "Blaby"                              
##  [21] "Blackburn with Darwen"              
##  [22] "Blackpool"                          
##  [23] "Bolsover"                           
##  [24] "Bolton"                             
##  [25] "Boston"                             
##  [26] "Bournemouth, Christchurch and Poole"
##  [27] "Bracknell Forest"                   
##  [28] "Bradford"                           
##  [29] "Braintree"                          
##  [30] "Breckland"                          
##  [31] "Brent"                              
##  [32] "Brentwood"                          
##  [33] "Brighton and Hove"                  
##  [34] "Bristol, City of"                   
##  [35] "Broadland"                          
##  [36] "Bromley"                            
##  [37] "Bromsgrove"                         
##  [38] "Broxbourne"                         
##  [39] "Broxtowe"                           
##  [40] "Burnley"                            
##  [41] "Bury"                               
##  [42] "Calderdale"                         
##  [43] "Cambridge"                          
##  [44] "Camden"                             
##  [45] "Cannock Chase"                      
##  [46] "Canterbury"                         
##  [47] "Carlisle"                           
##  [48] "Castle Point"                       
##  [49] "Central Bedfordshire"               
##  [50] "Charnwood"                          
##  [51] "Chelmsford"                         
##  [52] "Cheltenham"                         
##  [53] "Cherwell"                           
##  [54] "Cheshire East"                      
##  [55] "Cheshire West and Chester"          
##  [56] "Chesterfield"                       
##  [57] "Chichester"                         
##  [58] "Chiltern"                           
##  [59] "Chorley"                            
##  [60] "Colchester"                         
##  [61] "Copeland"                           
##  [62] "Corby"                              
##  [63] "Cornwall and Isles of Scilly"       
##  [64] "Cotswold"                           
##  [65] "County Durham"                      
##  [66] "Coventry"                           
##  [67] "Craven"                             
##  [68] "Crawley"                            
##  [69] "Croydon"                            
##  [70] "Dacorum"                            
##  [71] "Darlington"                         
##  [72] "Dartford"                           
##  [73] "Daventry"                           
##  [74] "Derby"                              
##  [75] "Derbyshire Dales"                   
##  [76] "Doncaster"                          
##  [77] "Dorset"                             
##  [78] "Dover"                              
##  [79] "Dudley"                             
##  [80] "Ealing"                             
##  [81] "East Cambridgeshire"                
##  [82] "East Devon"                         
##  [83] "East Hampshire"                     
##  [84] "East Hertfordshire"                 
##  [85] "East Lindsey"                       
##  [86] "East Northamptonshire"              
##  [87] "East Riding of Yorkshire"           
##  [88] "East Staffordshire"                 
##  [89] "East Suffolk"                       
##  [90] "Eastbourne"                         
##  [91] "Eastleigh"                          
##  [92] "Eden"                               
##  [93] "Elmbridge"                          
##  [94] "Enfield"                            
##  [95] "Epping Forest"                      
##  [96] "Epsom and Ewell"                    
##  [97] "Erewash"                            
##  [98] "Exeter"                             
##  [99] "Fareham"                            
## [100] "Fenland"                            
## [101] "Folkestone and Hythe"               
## [102] "Forest of Dean"                     
## [103] "Fylde"                              
## [104] "Gateshead"                          
## [105] "Gedling"                            
## [106] "Gloucester"                         
## [107] "Gosport"                            
## [108] "Gravesham"                          
## [109] "Great Yarmouth"                     
## [110] "Greenwich"                          
## [111] "Guildford"                          
## [112] "Hackney and City of London"         
## [113] "Halton"                             
## [114] "Hambleton"                          
## [115] "Hammersmith and Fulham"             
## [116] "Harborough"                         
## [117] "Haringey"                           
## [118] "Harlow"                             
## [119] "Harrogate"                          
## [120] "Harrow"                             
## [121] "Hart"                               
## [122] "Hartlepool"                         
## [123] "Hastings"                           
## [124] "Havant"                             
## [125] "Havering"                           
## [126] "Herefordshire, County of"           
## [127] "Hertsmere"                          
## [128] "High Peak"                          
## [129] "Hillingdon"                         
## [130] "Hinckley and Bosworth"              
## [131] "Horsham"                            
## [132] "Hounslow"                           
## [133] "Huntingdonshire"                    
## [134] "Hyndburn"                           
## [135] "Ipswich"                            
## [136] "Isle of Wight"                      
## [137] "Islington"                          
## [138] "Kensington and Chelsea"             
## [139] "Kettering"                          
## [140] "King's Lynn and West Norfolk"       
## [141] "Kingston upon Hull, City of"        
## [142] "Kingston upon Thames"               
## [143] "Kirklees"                           
## [144] "Knowsley"                           
## [145] "Lambeth"                            
## [146] "Lancaster"                          
## [147] "Leeds"                              
## [148] "Leicester"                          
## [149] "Lewes"                              
## [150] "Lewisham"                           
## [151] "Lichfield"                          
## [152] "Lincoln"                            
## [153] "Liverpool"                          
## [154] "Luton"                              
## [155] "Maidstone"                          
## [156] "Maldon"                             
## [157] "Malvern Hills"                      
## [158] "Manchester"                         
## [159] "Mansfield"                          
## [160] "Medway"                             
## [161] "Melton"                             
## [162] "Mendip"                             
## [163] "Merton"                             
## [164] "Mid Devon"                          
## [165] "Mid Suffolk"                        
## [166] "Mid Sussex"                         
## [167] "Middlesbrough"                      
## [168] "Milton Keynes"                      
## [169] "Mole Valley"                        
## [170] "New Forest"                         
## [171] "Newark and Sherwood"                
## [172] "Newcastle upon Tyne"                
## [173] "Newcastle-under-Lyme"               
## [174] "Newham"                             
## [175] "North Devon"                        
## [176] "North East Derbyshire"              
## [177] "North East Lincolnshire"            
## [178] "North Hertfordshire"                
## [179] "North Kesteven"                     
## [180] "North Lincolnshire"                 
## [181] "North Norfolk"                      
## [182] "North Somerset"                     
## [183] "North Tyneside"                     
## [184] "North Warwickshire"                 
## [185] "North West Leicestershire"          
## [186] "Northampton"                        
## [187] "Northumberland"                     
## [188] "Norwich"                            
## [189] "Nottingham"                         
## [190] "Nuneaton and Bedworth"              
## [191] "Oadby and Wigston"                  
## [192] "Oldham"                             
## [193] "Oxford"                             
## [194] "Pendle"                             
## [195] "Peterborough"                       
## [196] "Plymouth"                           
## [197] "Portsmouth"                         
## [198] "Preston"                            
## [199] "Reading"                            
## [200] "Redbridge"                          
## [201] "Redcar and Cleveland"               
## [202] "Redditch"                           
## [203] "Reigate and Banstead"               
## [204] "Ribble Valley"                      
## [205] "Richmond upon Thames"               
## [206] "Richmondshire"                      
## [207] "Rochdale"                           
## [208] "Rochford"                           
## [209] "Rossendale"                         
## [210] "Rother"                             
## [211] "Rotherham"                          
## [212] "Rugby"                              
## [213] "Runnymede"                          
## [214] "Rushcliffe"                         
## [215] "Rushmoor"                           
## [216] "Rutland"                            
## [217] "Ryedale"                            
## [218] "Salford"                            
## [219] "Sandwell"                           
## [220] "Scarborough"                        
## [221] "Sedgemoor"                          
## [222] "Sefton"                             
## [223] "Selby"                              
## [224] "Sevenoaks"                          
## [225] "Sheffield"                          
## [226] "Shropshire"                         
## [227] "Slough"                             
## [228] "Solihull"                           
## [229] "Somerset West and Taunton"          
## [230] "South Bucks"                        
## [231] "South Cambridgeshire"               
## [232] "South Derbyshire"                   
## [233] "South Gloucestershire"              
## [234] "South Hams"                         
## [235] "South Holland"                      
## [236] "South Kesteven"                     
## [237] "South Lakeland"                     
## [238] "South Norfolk"                      
## [239] "South Northamptonshire"             
## [240] "South Oxfordshire"                  
## [241] "South Ribble"                       
## [242] "South Somerset"                     
## [243] "South Staffordshire"                
## [244] "South Tyneside"                     
## [245] "Southampton"                        
## [246] "Southend-on-Sea"                    
## [247] "Southwark"                          
## [248] "Spelthorne"                         
## [249] "St Albans"                          
## [250] "St. Helens"                         
## [251] "Stafford"                           
## [252] "Staffordshire Moorlands"            
## [253] "Stevenage"                          
## [254] "Stockport"                          
## [255] "Stockton-on-Tees"                   
## [256] "Stoke-on-Trent"                     
## [257] "Stratford-on-Avon"                  
## [258] "Stroud"                             
## [259] "Sunderland"                         
## [260] "Surrey Heath"                       
## [261] "Sutton"                             
## [262] "Swale"                              
## [263] "Swindon"                            
## [264] "Tameside"                           
## [265] "Tamworth"                           
## [266] "Tandridge"                          
## [267] "Teignbridge"                        
## [268] "Telford and Wrekin"                 
## [269] "Tendring"                           
## [270] "Test Valley"                        
## [271] "Tewkesbury"                         
## [272] "Thanet"                             
## [273] "Three Rivers"                       
## [274] "Thurrock"                           
## [275] "Tonbridge and Malling"              
## [276] "Torbay"                             
## [277] "Torridge"                           
## [278] "Tower Hamlets"                      
## [279] "Trafford"                           
## [280] "Tunbridge Wells"                    
## [281] "Uttlesford"                         
## [282] "Vale of White Horse"                
## [283] "Wakefield"                          
## [284] "Walsall"                            
## [285] "Waltham Forest"                     
## [286] "Wandsworth"                         
## [287] "Warrington"                         
## [288] "Warwick"                            
## [289] "Watford"                            
## [290] "Waverley"                           
## [291] "Wealden"                            
## [292] "Wellingborough"                     
## [293] "Welwyn Hatfield"                    
## [294] "West Berkshire"                     
## [295] "West Devon"                         
## [296] "West Lancashire"                    
## [297] "West Lindsey"                       
## [298] "West Oxfordshire"                   
## [299] "West Suffolk"                       
## [300] "Westminster"                        
## [301] "Wigan"                              
## [302] "Wiltshire"                          
## [303] "Winchester"                         
## [304] "Windsor and Maidenhead"             
## [305] "Wirral"                             
## [306] "Woking"                             
## [307] "Wokingham"                          
## [308] "Wolverhampton"                      
## [309] "Worcester"                          
## [310] "Worthing"                           
## [311] "Wychavon"                           
## [312] "Wycombe"                            
## [313] "Wyre"                               
## [314] "Wyre Forest"                        
## [315] "York"
t1 <- c("Cornwall and Isles of Scilly", "Isle of Wight", "Liverpool", "Swale", "Kingston upon Hull, City of", "Manchester", "South Cambridgeshire")

dsr_plot <- test$dsr %>%
  #filter(areaName %in% t1) %>%
  ggplot(aes(date, value, colour = areaName)) +
  geom_line(show.legend = FALSE) +
  labs(y = "Standardised case rate", 
       x = "Date", 
       title = "Age standardised 7-day rolling case rates per 100,000") +
  scale_x_date(breaks = "months") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1), 
        plot.title.position = "plot", 
        panel.background = element_blank())

library(plotly)
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ggplotly(dsr_plot)